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- EMDB-8633: CryoEM Structure of a Prokaryotic Cyclic Nucleotide-Gated Ion Channel -

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Basic information

Entry
Database: EMDB / ID: 8633
TitleCryoEM Structure of a Prokaryotic Cyclic Nucleotide-Gated Ion Channel
SampleLliK
SourceLeptospira licerasiae serovar varillal str. var 010 / bacteria
Map dataUnsharpened map
Methodsingle particle reconstruction, at 4.2 Å resolution
AuthorsJames ZM / Borst AJ
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, 4430-4435

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 4430-4435 Yorodumi Papers
CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel.
Zachary M James / Andrew J Borst / Yoni Haitin / Brandon Frenz / Frank DiMaio / William N Zagotta / David Veesler

Validation ReportPDB-ID: 5v4s

SummaryFull reportAbout validation report
DateDeposition: Mar 10, 2017 / Header (metadata) release: Mar 22, 2017 / Map release: Apr 12, 2017 / Last update: May 10, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 0.024
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5v4s
  • Surface level: 0.024
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_8633.map.gz (map file in CCP4 format, 49949 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
232 pix
1.37 Å/pix.
= 316.796 Å
232 pix
1.37 Å/pix.
= 316.796 Å
232 pix
1.37 Å/pix.
= 316.796 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.3655 Å
Density
Contour Level:0.024 (by author), 0.024 (movie #1):
Minimum - Maximum-0.023005761 - 0.061287668
Average (Standard dev.)0.0003627006 (0.0031903565)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions232232232
Origin000
Limit231231231
Spacing232232232
CellA=B=C: 316.796 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.36551.36551.3655
M x/y/z232232232
origin x/y/z0.0000.0000.000
length x/y/z316.796316.796316.796
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS232232232
D min/max/mean-0.0230.0610.000

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Supplemental data

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Sample components

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Entire LliK

EntireName: LliK / Number of components: 2
MassTheoretical: 200 kDa

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Component #1: protein, LliK

ProteinName: LliK / Recombinant expression: No
MassTheoretical: 200 kDa
SourceSpecies: Leptospira licerasiae serovar varillal str. var 010 / bacteria
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, LliK

ProteinName: LliK / Recombinant expression: No
Source (engineered)Expression System: Leptospira licerasiae serovar varillal str. var 010 / bacteria

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.9 mg/ml / pH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 18737
3D reconstructionSoftware: Relion / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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